9GCB

DUF4198 protein from Ideonella sakaiensis with Ni bound

Summary for 9GCB

• Entry DOI: 10.2210/pdb9gcb/pdb
• Descriptor: Nickel ECF transporter, additional periplasmic component NikK, NICKEL (II) ION, MALONATE ION, ... (4 entities in total)
• Functional Keywords: metalloprotein, oxygenase, peroxygenase, metal binding protein
• Biological source: Piscinibacter sakaiensis
• Total number of polymer chains: 2
• Total formula weight: 44947.75

Authors

Franco Cairo, J.P.L.,Correa, T.L.R.,Offen, W.A.,Nairn, A.,Walton, J.,Davies, G.J.,Walton, P.H.,Sweeney, S.T. (deposition date: 2024-08-01, release date: 2025-09-10, Last modification date: 2025-10-29)

Primary citation

Franco Cairo, J.P.L.,Correa, T.L.R.,Offen, W.A.,Nairn, A.K.,Walton, J.,Sweeney, S.T.,Davies, G.J.,Walton, P.H.
Signal-strapping as a protein-sequence search method for the discovery of metalloproteins.
Nat Commun, 16:9244-9244, 2025

PubMed Abstract: Metalloprotein discovery is often made post hoc, in which activity studies following protein isolation reveal a metal-ion dependence. Herein we take a different approach to finding metalloproteins, by building on the discovery of copper-containing lytic polysaccharide monooxygenases (LPMOs), which include an N-terminal histidine as part of their sequence. This residue acts as a natural chelator for transition metal ions, irrespective of the structure of the protein. We report the method of signal strapping, where sequences of N-terminal signal peptides artificially appended with a histidine residue at their C-terminus are used to bootstrap a proteomic search. These searches return sequences of proteins with an N-terminal histidine capable of coordinating a metal ion. We exemplify the approach by the discovery and characterisation of four classes of bacterial metalloproteins, including two that we denote as anglerases reflecting their potential to capture transition metal ions from the bacterial environment.

PubMed: 41115942
DOI: 10.1038/s41467-025-64309-x

Experimental method

X-RAY DIFFRACTION (1.44 Å)